1KW6

Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 1.45 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Batch7.5285Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
3.1561

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.829α = 90
b = 121.829β = 90
c = 109.357γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4526.0899.90.0630.0637.88.77245872435
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.5399.90.3730.37323.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4587.7168780365499.840.16340.1630.17102RANDOM11.595
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.335
r_dihedral_angle_1_deg4.961
r_scangle_it2.733
r_angle_other_deg2.135
r_scbond_it1.696
r_sphericity_free1.461
r_angle_refined_deg1.4
r_mcangle_it1.125
r_symmetry_hbond_refined0.654
r_mcbond_it0.597
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.335
r_dihedral_angle_1_deg4.961
r_scangle_it2.733
r_angle_other_deg2.135
r_scbond_it1.696
r_sphericity_free1.461
r_angle_refined_deg1.4
r_mcangle_it1.125
r_symmetry_hbond_refined0.654
r_mcbond_it0.597
r_symmetry_vdw_refined0.313
r_symmetry_vdw_other0.23
r_nbd_refined0.221
r_nbtor_other0.221
r_nbd_other0.198
r_xyhbond_nbd_refined0.151
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2229
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms31

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling